← Back to variant description
GeneBe API Showcase
This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.
API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.
Documentation & Advanced Usage
• Complete API documentation:docs.genebe.net/docs/api/overview/
• Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/
• Python client for pandas:pypi.org/project/genebe/
• Java CLI for VCF files:github.com/pstawinski/genebe-cli
• All tools documented at:docs.genebe.net
API Request Examples for Variant: 3-53092496-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=53092496&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 53092496,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000296292.8",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFT1",
"gene_hgnc_id": 30220,
"hgvs_c": "c.1331C>T",
"hgvs_p": "p.Thr444Met",
"transcript": "NM_052859.4",
"protein_id": "NP_443091.1",
"transcript_support_level": null,
"aa_start": 444,
"aa_end": null,
"aa_length": 541,
"cds_start": 1331,
"cds_end": null,
"cds_length": 1626,
"cdna_start": 1366,
"cdna_end": null,
"cdna_length": 5081,
"mane_select": "ENST00000296292.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFT1",
"gene_hgnc_id": 30220,
"hgvs_c": "c.1331C>T",
"hgvs_p": "p.Thr444Met",
"transcript": "ENST00000296292.8",
"protein_id": "ENSP00000296292.3",
"transcript_support_level": 1,
"aa_start": 444,
"aa_end": null,
"aa_length": 541,
"cds_start": 1331,
"cds_end": null,
"cds_length": 1626,
"cdna_start": 1366,
"cdna_end": null,
"cdna_length": 5081,
"mane_select": "NM_052859.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000272305",
"gene_hgnc_id": null,
"hgvs_c": "n.194C>T",
"hgvs_p": null,
"transcript": "ENST00000607283.5",
"protein_id": "ENSP00000475819.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 690,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFT1",
"gene_hgnc_id": 30220,
"hgvs_c": "c.1214C>T",
"hgvs_p": "p.Thr405Met",
"transcript": "ENST00000394738.7",
"protein_id": "ENSP00000378223.3",
"transcript_support_level": 5,
"aa_start": 405,
"aa_end": null,
"aa_length": 502,
"cds_start": 1214,
"cds_end": null,
"cds_length": 1509,
"cdna_start": 1267,
"cdna_end": null,
"cdna_length": 1800,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFT1",
"gene_hgnc_id": 30220,
"hgvs_c": "c.674C>T",
"hgvs_p": "p.Thr225Met",
"transcript": "XM_011534216.4",
"protein_id": "XP_011532518.1",
"transcript_support_level": null,
"aa_start": 225,
"aa_end": null,
"aa_length": 322,
"cds_start": 674,
"cds_end": null,
"cds_length": 969,
"cdna_start": 721,
"cdna_end": null,
"cdna_length": 4436,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "RFT1",
"gene_hgnc_id": 30220,
"hgvs_c": "c.1208+6885C>T",
"hgvs_p": null,
"transcript": "ENST00000850556.1",
"protein_id": "ENSP00000520849.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 465,
"cds_start": -4,
"cds_end": null,
"cds_length": 1398,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3963,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000272305",
"gene_hgnc_id": null,
"hgvs_c": "n.72-6644C>T",
"hgvs_p": null,
"transcript": "ENST00000607203.1",
"protein_id": "ENSP00000475866.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 768,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000272305",
"gene_hgnc_id": null,
"hgvs_c": "n.71+6885C>T",
"hgvs_p": null,
"transcript": "ENST00000607495.5",
"protein_id": "ENSP00000475958.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 823,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "RFT1",
"gene_hgnc_id": 30220,
"hgvs_c": "c.1208+6885C>T",
"hgvs_p": null,
"transcript": "XM_011534214.3",
"protein_id": "XP_011532516.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 477,
"cds_start": -4,
"cds_end": null,
"cds_length": 1434,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 9901,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "RFT1",
"gene_hgnc_id": 30220,
"hgvs_c": "c.1208+6885C>T",
"hgvs_p": null,
"transcript": "XM_011534215.4",
"protein_id": "XP_011532517.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 464,
"cds_start": -4,
"cds_end": null,
"cds_length": 1395,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7680,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "RFT1",
"gene_hgnc_id": 30220,
"hgvs_c": "c.1209-6644C>T",
"hgvs_p": null,
"transcript": "XM_006713384.4",
"protein_id": "XP_006713447.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 403,
"cds_start": -4,
"cds_end": null,
"cds_length": 1212,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3157,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "RFT1",
"gene_hgnc_id": 30220,
"hgvs_c": "n.1243+6885C>T",
"hgvs_p": null,
"transcript": "XR_007095765.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7870,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "RFT1",
"gene_hgnc_id": 30220,
"dbsnp": "rs147740901",
"frequency_reference_population": 0.000513496,
"hom_count_reference_population": 4,
"allele_count_reference_population": 828,
"gnomad_exomes_af": 0.000526666,
"gnomad_genomes_af": 0.000387271,
"gnomad_exomes_ac": 769,
"gnomad_genomes_ac": 59,
"gnomad_exomes_homalt": 4,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.053609758615493774,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.25,
"revel_prediction": "Benign",
"alphamissense_score": 0.081,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.24,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.469,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.02,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -9,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BS1_Supporting,BS2",
"acmg_by_gene": [
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BS1_Supporting",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000296292.8",
"gene_symbol": "RFT1",
"hgnc_id": 30220,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1331C>T",
"hgvs_p": "p.Thr444Met"
},
{
"score": -8,
"benign_score": 8,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000607283.5",
"gene_symbol": "ENSG00000272305",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.194C>T",
"hgvs_p": null
}
],
"clinvar_disease": "Inborn genetic diseases,RFT1-congenital disorder of glycosylation,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:7",
"phenotype_combined": "RFT1-congenital disorder of glycosylation|Inborn genetic diseases|not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}